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Open data
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Basic information
Entry | Database: PDB / ID: 7ysi | ||||||
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Title | Crystal structure of thioredoxin 2 | ||||||
![]() | Thiol disulfide reductase thioredoxin | ||||||
![]() | OXIDOREDUCTASE / Trx2 / thioredoxin2 | ||||||
Function / homology | Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / protein-disulfide reductase activity / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Thiol disulfide reductase thioredoxin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chang, Y.J. / Park, H.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Comparison of the structure and activity of thioredoxin 2 and thioredoxin 1 from Acinetobacter baumannii. Authors: Chang, Y.J. / Sung, J.H. / Lee, C.S. / Lee, J.H. / Park, H.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.5 KB | Display | ![]() |
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PDB format | ![]() | 52.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3p2aS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16736.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: trxC, AYR68_15440, B7L45_02985, BAA1790NC_0521, BS065_02615, CBL15_02595, CTZ19_02595, D8O08_003970, DLI71_14475, DLI72_02635, E2532_03525, E2533_03310, E2534_07555, E2535_02615, E2536_10370, ...Gene: trxC, AYR68_15440, B7L45_02985, BAA1790NC_0521, BS065_02615, CBL15_02595, CTZ19_02595, D8O08_003970, DLI71_14475, DLI72_02635, E2532_03525, E2533_03310, E2534_07555, E2535_02615, E2536_10370, E2538_07040, E2539_06760, E2540_11860, E2541_06480, EA720_013275, FDN00_17805, FE003_02610, IAG11_14015 Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES/NaOH pH 7.0, 15% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 125 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.202→27.42 Å / Num. obs: 45597 / % possible obs: 96.64 % / Redundancy: 12.7 % / Biso Wilson estimate: 14.86 Å2 / Rmerge(I) obs: 0.09366 / Net I/σ(I): 15.42 |
Reflection shell | Resolution: 1.202→27.42 Å / Rmerge(I) obs: 2.435 / Num. unique obs: 4106 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3p2a Resolution: 1.202→27.418 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.49 Å2 / Biso mean: 19.4527 Å2 / Biso min: 9.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.202→27.418 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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